mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 07:19:13 +08:00
Nicola Soranzo
53f14908ef
Fix:
```
def test_deserialize_xml_tool(tool_app):
> tool = _deserialize(tool_app, tool_source_class='XmlToolSource', raw_tool_source=XML_TOOL)
test/unit/app/tools/test_tool_deserialization.py:59:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
test/unit/app/tools/test_tool_deserialization.py:54: in _deserialize
return create_tool_from_source(app, tool_source=tool_source)
lib/galaxy/tools/__init__.py:278: in create_tool_from_source
tool = ToolClass(config_file, tool_source, app, **kwds)
lib/galaxy/tools/__init__.py:606: in __init__
raise e
lib/galaxy/tools/__init__.py:603: in __init__
self.parse(tool_source, guid=guid, dynamic=dynamic)
if has_missing_data:
biotools_reference = self.biotools_reference
> metadata_source = self.app.biotools_metadata_source
E AttributeError: 'ToolApp' object has no attribute 'biotools_metadata_source'
lib/galaxy/tools/__init__.py:1032: AttributeError
```
introduced merging forward https://github.com/galaxyproject/galaxy/pull/13202 .
75 lines
1.8 KiB
Python
75 lines
1.8 KiB
Python
import pytest
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from galaxy.model.unittest_utils import GalaxyDataTestApp
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from galaxy.tool_util.parser import get_tool_source
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from galaxy.tool_util.parser.cwl import CwlToolSource
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from galaxy.tools import create_tool_from_source
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XML_TOOL = """
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<tool id="tool_id" name="xml tool" version="1"/>
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"""
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CWL_TOOL = """
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cwlVersion: v1.0
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class: CommandLineTool
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baseCommand: echo
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inputs:
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message:
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type: string
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inputBinding:
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position: 1
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outputs: []
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"""
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YAML_TOOL = """
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id: simple_constructs_y
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name: simple_constructs_y
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version: 1.0
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command:
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>
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echo "$booltest" >> $out_file1;
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inputs:
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- name: booltest
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type: boolean
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truevalue: booltrue
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falsevalue: boolfalse
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checked: false
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outputs:
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out_file1:
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format: txt
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"""
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class ToolApp(GalaxyDataTestApp):
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name = 'galaxy'
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biotools_metadata_source = None
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job_search = None
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@pytest.fixture
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def tool_app():
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return ToolApp()
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def _deserialize(app, tool_source_class, raw_tool_source):
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tool_source = get_tool_source(tool_source_class=tool_source_class, raw_tool_source=raw_tool_source)
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assert type(tool_source).__name__ == tool_source_class
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return create_tool_from_source(app, tool_source=tool_source)
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def test_deserialize_xml_tool(tool_app):
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tool = _deserialize(tool_app, tool_source_class='XmlToolSource', raw_tool_source=XML_TOOL)
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assert tool.id == 'tool_id'
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assert tool.name == 'xml tool'
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def test_deserialize_yaml_tool(tool_app):
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tool = _deserialize(tool_app, tool_source_class='YamlToolSource', raw_tool_source=YAML_TOOL)
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assert tool.id == 'simple_constructs_y'
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assert tool.name == 'simple_constructs_y'
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def test_deserialize_cwl_tool(tool_app):
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# Can't verify much about cwl tools at this point
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tool_source = get_tool_source(tool_app, tool_source_class='CwlToolSource', raw_tool_source=CWL_TOOL)
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assert isinstance(tool_source, CwlToolSource)
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